DOVER — Officials around Great Bay are vowing to continue fighting against the new wastewater treatment standards being handed down by the Environmental Protection Agency, despite the fact that one community recently agreed to comply with the federal agency.

Officials in Newmarket announced Monday the town has agreed to meet the strict new cap on nitrogen discharge being phased in around the Seacoast by the EPA.

Communities around Great Bay have butted heads with the EPA over the issue during the last two years. They argue federal regulators and state officials are relying on outdated science to reach their conclusions about the nutrient problems in Great Bay.

Newmarket previously joined with Dover, Exeter, Portsmouth and Rochester to file a lawsuit against state environmental officials over the issue. Members of the so-called “Great Bay Municipal Coalition” were hoping to force a scientific review of the new nitrogen standards.

The communities agree that nitrogen discharge into the Great Bay watershed should be reduced, but they argue a higher threshold should be allowed. They point out that meeting the EPA's nitrogen limits will require them to invest millions of additional dollars into wastewater treatment facilities.

Their lawsuit was thrown out by a Merrimack County Superior Court judge, but the plaintiffs filed for reconsideration last month.

“The overall concern with all of the coalition communities, all along, has been to make sure what is necessary to protect Great Bay and that we spend public money in the right way,” Dover City Manager Michael Joyal said this week.

If anything, Joyal said, the communities are encouraged that the EPA and Department of Environmental Services acknowledged in their agreement with Newmarket that “more science is in fact needed to determine if the 3 milligrams per liter in the permit is appropriate.”

The EPA has called for Newmarket and other Great Bay communities to cap nitrogen discharge at 3 milligrams per liter. Members of the Great Bay Municipal Coalition have asked the EPA to consider issuing wastewater discharge permits that cap nitrogen at 8 milligrams per liter, a level more easily attainable.

Under the terms of its agreement with the EPA, Newmarket's final permit discharge limit has been set at 3 mg/l, but the community might not ultimately be held to that standard. The EPA has granted Newmarket 15 years to achieve the new level, and an interim limit of 8.0 mg/l will be in place until then.

The agreement also incorporates an “adaptive management approach.” The EPA will study the nitrogen levels in Great Bay for five years after Newmarket's new facility is operational, according to town officials. The additional monitoring period “may lead to a conclusion that the 3.0 mg/l limit is more stringent than it needs to be,” and if so, the EPA will drop the 3.0 mg/l requirement, an announcement from Newmarket officials states.

Dover's plan essentially utilizes the existing wastewater treatment plant. Some equipment will be replaced to reach a level of at least 8 milligrams per liter. That initial investment would likely take place regardless of the EPA's new limits. Additional facilities, such as tanks and new pumps, would have to be constructed to get down to at least 3 milligrams per liter during the portion of the year required by the EPA.

“What the problem is, with federal law, is that once the standard is set, in the Clean Water Act, it is almost impossible for the EPA to say, 'We can do something else now,' Joyal said. “It is difficult to back the standard up. That is the concern that all the communities have, is that, if you are willing to have the communities built at 8 milligrams per liter and study the science, then why not set the limit in the permit to 8 milligrams per liter?”

John Hall, principal at Hall & Associates, the environmental firm that has advised the Great Bay coalition, said he plans to speak with community leaders this week to assess legal options. He pointed out that Newmarket officials still maintain they are uneasy with the scientific basis of the EPA's permit.

“The real issue that remains on the table, and I think it's obvious also from Newmarket, whatever settlement they've reached, is the communities disagree on the science, and want to have a fair review of the updated scientific information,” Hall said. “That, in the end, is what this is all about. If the new science shows that EPA's position is, in fact, correct, and needs to be implemented, all of the communities are going to step up and do what they need to do.”

Rochester City Manager Daniel Fitzpatrick said Newmarket's decision isn't a reflection of the circumstances facing Rochester. The city will need to pay about $20 million to reach the 3 milligram per liter limit, he said.

“What Newmarket does is Newmarket's business,” he said.

“Every community is different,” said Portsmouth Mayor Eric Spear, “and they're located different places in the watershed, they have different populations, their sewage is a different make-up ...”

Spear pointed out that Portsmouth is also “moving aggressively” to tackle wastewater challenges now, and designing a new multimillion dollar wastewater plant on Peirce Island. “We're moving full speed ahead on all of these issues,” Spear said.